This is Steven Salzberg's blog on genomics, pseudoscience, medical breakthroughs, higher education, and other topics, including skepticism about unscientific medical practices. Here's where I can say what I really think about abuses and distortions of science, wherever I see them.

But it took The Lancet 12 years to retract the paper, and in that time the anti-vaccine movement flourished. Wakefield became a hero within that movement, and continues to push his anti-vaccine propaganda today, even making films presenting himself as a lone hero fighting for truth.

Other anti-vaxxers are very familiar with this saga, and they have followed Wakefield's recipe by writing scientific papers and attempting to get them published in reputable journals. Usually they fail, but now and then one slips through, which they then point to as "proof" that vaccines are harmful.

The latest example is a paper that appeared in Scientific Reports in November 2016 and that the journal just retracted last week. It has a title that sounds highly technical: "Murine hypothalamic destruction with vascular cell apoptosis subsequent to combined administration of human papilloma virus vaccine and pertussis toxin." (Wakefield's 1998 paper had a similarly obscure title.)

(Aside: the HPV vaccine protects people from human papillomavirus, which causes many cases of cervical cancer as well as throat cancer. It's the first vaccine that prevents these cancers, which is an amazing breakthrough. Millions of doses have been administered with essentially zero cases of harm.)

What did the paper do? Basically, it was a setup. The authors–most of them from Tokyo Medical University–gave mice a huge dose of HPV vaccine plus (here's the kicker) a large dose of pertussis toxin. There's no valid reason to administer that toxin except to try to induce brain damage, which the authors could then blame on the HPV vaccine. The study design was clearly awful, and the paper should never have been published.

What was not publicly known before now was that I too wrote to the journal editors, asking them to "take action quickly, rather than waiting for over 10 years as The Lancet did." First I wrote to the immunology sub-editor, who forwarded my letter to the Editor-in-Chief, Richard White. Dr. White replied on 29 Nov 2016 that "We are looking into the specific issues raised regarding this paper."

That was the last I heard of it, until the journal announced last week that they have retracted the paper.

So in the end, the scientific record was corrected. But why did it take Scientific Reports 18 months to do it? Haven't they learned from the Wakefield debacle how much damage can be done while antivaccine articles like this one remain in the literature? The journal's editors had a responsibility to act more quickly, and they failed. The scientists who wrote those letters back in 2016 had the same complaint, as reported by Dennis Normile in Science last week. Not surprisingly, Scientific Reports refused to comment (when asked by Science) on any details of their review process.

That's not good enough. Scientific Reports is a "mega-journal," a new type of journal that publishes thousands of papers per year, with a relatively low bar for acceptance. The idea (not a bad one, in theory) is that any valid scientific study, even one that makes only a very small contribution, still merits publication somewhere.

What publishers have learned is that these mega-journals are very profitable, because they charge a publishing fee that more than covers their costs. In return for these profits, Nature Publishing has an obligation to remove harmful papers far faster than they did in this case. Otherwise, it's only a matter of time before anti-vaxxers do this again.

Finally, let me repeat something that can't be said often enough: vaccines are perhaps the single greatest medical advance in human history. They have saved millions of lives, and they continue to save lives today. Scourges such as smallpox and polio, which once swept through populations causing terrible pain, suffering, and death, have been conquered thanks to vaccines. Medical researchers continue to work on new vaccines against the infections that still plague us, and they are the real heroes.

You would think that the editors of the top science journals in the world would know how to write clearly. But if you read their joint statement in the journal Science last week, you might be forgiven for wondering what the heck they are talking about. It's not that complicated, really. Let me explain.

"The era of secret science at EPA is coming to an end. The ability to test, authenticate, and reproduce scientific findings is vital for the integrity of rulemaking process."

The press release, which is titled "EPA Administrator Pruitt Proposes Rule To Strengthen Science Used In EPA Regulations", seems to be all about science and openness. One thing I've got to give them credit for: the PR people at the EPA know how to obfuscate.

It turns out this is just a ruse. As Pruitt certainly knows, many of the EPA's rules are based on studies of human subjects, which are governed by strict privacy rules–which are necessary not only to get people to participate in the studies, but also because violating people's privacy can be highly unethical. This means that many studies showing the harms of pollution–for example, this massive study, which found that fine-scale particulate matter from coal plants increases the risk of lung and heart disease–are not "transparent" enough for the EPA, because the identities of the participants as well as all their health records are confidential.

In other words, the new EPA policy isn't about scientific transparency. It's a transparent (!) attempt to ignore the negative health effects of pollution, so that Pruitt can put in place new rules allowing polluters to dump more pollutants into our air and water. See how that works?

In response, the Editors-in-Chief of Science, Nature, the Public Library of Science, and the Proceedings of the National Academy of Sciences issued a joint statement. Alas, their statement is anything but clear. They spend about three-fourths of it explaining about how they support data sharing, and finally, in their last sentence, they write this:

That's it. Even the most sophisticated reader could be forgiven for not understanding what the issue is, not from this statement alone.

Here's what they should have said: the EPA wants to ignore the health consequences of pollution when creating policy. The EPA administrator, Scott Pruitt, has announced a new policy that pretends to be about scientific transparency, but is nothing of the sort. Instead, this policy is designed to undermine the EPA's mission, which is (and you can read this right on the EPA's website "to protect human health and the environment."

Since the EPA's creation in 1970, the U.S. has made tremendous strides in cleaning up our air and water. Let's not start backsliding just to enhance the profits of a few polluters.

[Note: I have written the EPA and asked for comment. I will update this article if they respond.]